Larbat2016.1 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Base Model)

  public model
Model Identifier
BIOMD0000000857
Short description
This is a global mathematical model describing metabolic partitioning of carbon resources in plants between growth and defense, as a function of nitrate fertilization. The model hinges on the dynamics of sucrose inflow/outflow properties.
Format
SBML (L2V4)
Related Publication
  • Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light/dark conditions.
  • Larbat R, Robin C, Lillo C, Drengstig T, Ruoff P
  • Journal of theoretical biology , 8/ 2016 , Volume 402 , pages: 144-157 , PubMed ID: 27164436
  • INRA UMR 1121, Agronomie & Environnement Nancy-Colmar, TSA 40602, 54518 Vandoeuvre Cedex, France; Universit√© de Lorraine UMR 1121, Agronomie & Environnement Nancy-Colmar, TSA 40602, 54518 Vandoeuvre Cedex, France. Electronic address: romain.larbat@univ-lorraine.fr.
  • In plants, the partitioning of carbon resources between growth and defense is detrimental for their development. From a metabolic viewpoint, growth is mainly related to primary metabolism including protein, amino acid and lipid synthesis, whereas defense is based notably on the biosynthesis of a myriad of secondary metabolites. Environmental factors, such as nitrate fertilization, impact the partitioning of carbon resources between growth and defense. Indeed, experimental data showed that a shortage in the nitrate fertilization resulted in a reduction of the plant growth, whereas some secondary metabolites involved in plant defense, such as phenolic compounds, accumulated. Interestingly, sucrose, a key molecule involved in the transport and partitioning of carbon resources, appeared to be under homeostatic control. Based on the inflow/outflow properties of sucrose homeostatic regulation we propose a global model on how the diversion of the primary carbon flux into the secondary phenolic pathways occurs at low nitrate concentrations. The model can account for the accumulation of starch during the light phase and the sucrose remobilization by starch degradation during the night. Day-length sensing mechanisms for variable light-dark regimes are discussed, showing that growth is proportional to the length of the light phase. The model can describe the complete starch consumption during the night for plants adapted to a certain light/dark regime when grown on sufficient nitrate and can account for an increased accumulation of starch observed under nitrate limitation.
Contributors
Submitter of the first revision: Johannes Meyer
Submitter of this revision: Johannes Meyer
Modellers: Johannes Meyer

Metadata information

hasProperty (3 statements)
Mathematical Modelling Ontology Ordinary differential equation model
Gene Ontology sucrose metabolic process
Gene Ontology starch metabolic process


Curation status
Curated


Tags

Connected external resources

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Model files

Larbat2016.1.xml SBML L2V4 Representation of Larbat2016.1 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Base Model) 88.25 KB Preview | Download

Additional files

Larbat2016.1.cps COPASI file of Larbat2016.1 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Base Model) 140.76 KB Preview | Download
Larbat2016.1.sedml SED-ML file of Larbat2016.1 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Base Model) 3.91 KB Preview | Download

  • Model originally submitted by : Johannes Meyer
  • Submitted: Nov 13, 2019 4:50:23 PM
  • Last Modified: Nov 13, 2019 4:50:23 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Nov 13, 2019 4:50:23 PM
    • Submitted by: Johannes Meyer
    • With comment: Automatically added model identifier BIOMD0000000857
Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
Ephe

C49887 ; phenol
1.0E-5 mmol
sucr

sucrose
0.7 mmol
trioseP

CHEBI:27137 ; phosphorylated
1.1 mmol
Estarch

starch ; C49887
1.0E-4 mmol
ECO2

C49887 ; carbon dioxide
1.0 mmol
Reactions
Reactions Rate Parameters
Ephe => compartment*k7*Ephe/(k8+Ephe) k8 = 1.0E-6; k7 = 9.8
sucr => ; Ephe compartment*k9*sucr*Ephe*f_I_phe k9 = 1.0; f_I_phe = 0.0384615384615385
trioseP => sucr; EtrioseP compartment*k4*EtrioseP*trioseP k4 = 1.0
Estarch => ; sucr compartment*k35*sucr*Estarch/(k36+Estarch) k36 = 1.0E-4; k35 = 10.0
sucr => compartment*(k14+k15)*sucr k14 = 0.2; k15 = 0.2
starch => sucr; Estarch compartment*k37*starch*Estarch k37 = 0.1
=> Ephe; sucr compartment*k6*sucr*f_I_E_phe_outfl k6 = 10.0; f_I_E_phe_outfl = 0.995024875621891
=> ECO2 compartment*k30 k30 = 0.0
ECO2 => ; trioseP compartment*k31*trioseP*ECO2/(k32+ECO2) k32 = 1.0E-5; k31 = 0.0
trioseP => starch compartment*k10*trioseP k10 = 10.0
Curator's comment:
(added: 13 Nov 2019, 16:50:14, updated: 13 Nov 2019, 16:50:14)
Reproduced plot of Figure 2(b) in the original publication. Model simulated and plot produced using COPASI 4.24 (Build 197).